OpenMS  2.7.0
OpenMS::DIAHelpers Namespace Reference

Functions

bool integrateWindow (const OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &mz, double &intensity, bool centroided=false)
 Helper functions for the DIA scoring of OpenSWATH. More...
 
void integrateWindows (const OpenSwath::SpectrumPtr spectrum, const std::vector< double > &windows_center, double width, std::vector< double > &integrated_windows_intensity, std::vector< double > &integrated_windows_mz, bool remove_zero=false)
 Integrate intensities in a spectrum from start to end. More...
 
void integrateDriftSpectrum (OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &im, double &intensity, double drift_start, double drift_end)
 Integrate intensity in an ion mobility spectrum from start to end. More...
 
void adjustExtractionWindow (double &right, double &left, const double &mz_extract_window, const bool &mz_extraction_ppm)
 Adjust left/right window based on window and whether its ppm or not. More...
 
void getBYSeries (const AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, TheoreticalSpectrumGenerator const *g, int charge=1)
 compute the b and y series masses for a given AASequence More...
 
void getTheorMasses (const AASequence &a, std::vector< double > &masses, TheoreticalSpectrumGenerator const *g, int charge=1)
 for SWATH – get the theoretical b and y series masses for a sequence More...
 
void getAveragineIsotopeDistribution (const double product_mz, std::vector< std::pair< double, double > > &isotopes_spec, const int charge=1, const int nr_isotopes=4, const double mannmass=1.00048)
 get averagine distribution given mass More...
 
void simulateSpectrumFromAASequence (const AASequence &aa, std::vector< double > &first_isotope_masses, std::vector< std::pair< double, double > > &isotope_masses, TheoreticalSpectrumGenerator const *g, int charge=1)
 simulate spectrum from AASequence More...
 
void modifyMassesByCharge (const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, int charge=1)
 modify masses by charge More...
 
void addPreisotopeWeights (const std::vector< double > &first_isotope_masses, std::vector< std::pair< double, double > > &isotope_spec, UInt nr_peaks=2, double pre_isotope_peaks_weight=-0.5, double mannmass=1.000482, int charge=1)
 add (potentially negative) pre-isotope weights to spectrum More...
 
void addPreisotopeWeights (double mz, std::vector< std::pair< double, double > > &isotope_spec, UInt nr_peaks=2, double pre_isotope_peaks_weight=-0.5, double mannmass=1.000482, int charge=1)
 add negative pre-isotope weights to spectrum More...
 
void addIsotopes2Spec (const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotope_masses, Size nr_isotopes, int charge=1)
 
void addSinglePeakIsotopes2Spec (double mz, double ity, std::vector< std::pair< double, double > > &isotope_masses, Size nr_isotopes, int charge)
 
void sortByFirst (std::vector< std::pair< double, double > > &tmp)
 sorts vector of pairs by first More...
 
void extractFirst (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
 extract first from vector of pairs More...
 
void extractSecond (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
 extract second from vector of pairs More...
 

Function Documentation

◆ addIsotopes2Spec()

void OpenMS::DIAHelpers::addIsotopes2Spec ( const std::vector< std::pair< double, double > > &  spec,
std::vector< std::pair< double, double > > &  isotope_masses,
Size  nr_isotopes,
int  charge = 1 
)

given an experimental spectrum, add averagine isotope pattern for every peak. Old + new peaks are pushed to isotopeMasses

◆ addPreisotopeWeights() [1/2]

void OpenMS::DIAHelpers::addPreisotopeWeights ( const std::vector< double > &  first_isotope_masses,
std::vector< std::pair< double, double > > &  isotope_spec,
UInt  nr_peaks = 2,
double  pre_isotope_peaks_weight = -0.5,
double  mannmass = 1.000482,
int  charge = 1 
)

add (potentially negative) pre-isotope weights to spectrum

◆ addPreisotopeWeights() [2/2]

void OpenMS::DIAHelpers::addPreisotopeWeights ( double  mz,
std::vector< std::pair< double, double > > &  isotope_spec,
UInt  nr_peaks = 2,
double  pre_isotope_peaks_weight = -0.5,
double  mannmass = 1.000482,
int  charge = 1 
)

add negative pre-isotope weights to spectrum

◆ addSinglePeakIsotopes2Spec()

void OpenMS::DIAHelpers::addSinglePeakIsotopes2Spec ( double  mz,
double  ity,
std::vector< std::pair< double, double > > &  isotope_masses,
Size  nr_isotopes,
int  charge 
)

given a peak of experimental mz and intensity, add averagine isotope pattern to a "spectrum". Old + new peaks are pushed to isotopeMasses

◆ adjustExtractionWindow()

void OpenMS::DIAHelpers::adjustExtractionWindow ( double &  right,
double &  left,
const double &  mz_extract_window,
const bool &  mz_extraction_ppm 
)

Adjust left/right window based on window and whether its ppm or not.

◆ extractFirst()

void OpenMS::DIAHelpers::extractFirst ( const std::vector< std::pair< double, double > > &  peaks,
std::vector< double > &  mass 
)

extract first from vector of pairs

◆ extractSecond()

void OpenMS::DIAHelpers::extractSecond ( const std::vector< std::pair< double, double > > &  peaks,
std::vector< double > &  mass 
)

extract second from vector of pairs

◆ getAveragineIsotopeDistribution()

void OpenMS::DIAHelpers::getAveragineIsotopeDistribution ( const double  product_mz,
std::vector< std::pair< double, double > > &  isotopes_spec,
const int  charge = 1,
const int  nr_isotopes = 4,
const double  mannmass = 1.00048 
)

get averagine distribution given mass

◆ getBYSeries()

void OpenMS::DIAHelpers::getBYSeries ( const AASequence a,
std::vector< double > &  bseries,
std::vector< double > &  yseries,
TheoreticalSpectrumGenerator const *  g,
int  charge = 1 
)

compute the b and y series masses for a given AASequence

◆ getTheorMasses()

void OpenMS::DIAHelpers::getTheorMasses ( const AASequence a,
std::vector< double > &  masses,
TheoreticalSpectrumGenerator const *  g,
int  charge = 1 
)

for SWATH – get the theoretical b and y series masses for a sequence

◆ integrateDriftSpectrum()

void OpenMS::DIAHelpers::integrateDriftSpectrum ( OpenSwath::SpectrumPtr  spectrum,
double  mz_start,
double  mz_end,
double &  im,
double &  intensity,
double  drift_start,
double  drift_end 
)

Integrate intensity in an ion mobility spectrum from start to end.

This function will integrate the intensity in a spectrum between mz_start and mz_end, returning the total intensity and an intensity-weighted drift time value.

Note
If there is no signal, mz will be set to -1 and intensity to 0

◆ integrateWindow()

bool OpenMS::DIAHelpers::integrateWindow ( const OpenSwath::SpectrumPtr  spectrum,
double  mz_start,
double  mz_end,
double &  mz,
double &  intensity,
bool  centroided = false 
)

Helper functions for the DIA scoring of OpenSWATH.

Integrate intensity in a spectrum from start to end

This function will integrate the intensity in a spectrum between mz_start and mz_end, returning the total intensity and an intensity-weighted m/z value.

Note
If there is no signal, mz will be set to -1 and intensity to 0
Returns
Returns true if a signal was found (and false if no signal was found)

◆ integrateWindows()

void OpenMS::DIAHelpers::integrateWindows ( const OpenSwath::SpectrumPtr  spectrum,
const std::vector< double > &  windows_center,
double  width,
std::vector< double > &  integrated_windows_intensity,
std::vector< double > &  integrated_windows_mz,
bool  remove_zero = false 
)

Integrate intensities in a spectrum from start to end.

Parameters
[in]spectrumSpectrum
[in]windows_centercenter location

◆ modifyMassesByCharge()

void OpenMS::DIAHelpers::modifyMassesByCharge ( const std::vector< std::pair< double, double > > &  masses,
std::vector< std::pair< double, double > > &  modmass,
int  charge = 1 
)

modify masses by charge

Parameters
[in]modmass[out]

◆ simulateSpectrumFromAASequence()

void OpenMS::DIAHelpers::simulateSpectrumFromAASequence ( const AASequence aa,
std::vector< double > &  first_isotope_masses,
std::vector< std::pair< double, double > > &  isotope_masses,
TheoreticalSpectrumGenerator const *  g,
int  charge = 1 
)

simulate spectrum from AASequence

◆ sortByFirst()

void OpenMS::DIAHelpers::sortByFirst ( std::vector< std::pair< double, double > > &  tmp)

sorts vector of pairs by first